BN1974 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 5.8387e-09 1.6222e-05
Layer 2 9.8815e-08 1.2825e-03
Layer 3 3.7690e-07 5.6878e-05
Layer 5 2.3572e-06 7.0474e-04
Layer 6 5.1256e-05 6.2878e-03
Layer 1 4.5899e-01 4.8264e-01
WM 9.1762e-01 4.8203e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
GABBR2 Expression Distribution
Gene Specificity Score (GSS)
GABBR2 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
GABBR2 Layer 4 2.7363 0.7389
INA Layer 3 2.5059 0.7344
LINGO1 Layer 4 2.6309 0.7331
SNAP91 Layer 4 2.6191 0.7315
PTPRN2 Layer 4 2.3652 0.7296
SULT4A1 Layer 4 2.6133 0.7287
SYNGR3 Layer 4 2.4180 0.7263
MAPRE3 Layer 4 2.5566 0.7263
INPP5F Layer 4 2.8398 0.7210
KIF3A Layer 4 2.3711 0.7194
PNMA8A Layer 4 2.3184 0.7189
SYT13 Layer 4 2.7598 0.7185
DLGAP1 Layer 3 2.3867 0.7171
GABRG2 Layer 4 2.7910 0.7159
TUBB4B Layer 4 2.2520 0.7151
CACYBP Layer 4 2.4121 0.7149
SELENOH Layer 5 2.3438 0.7149
FHL1 Layer 4 2.5059 0.7142
PFKM Layer 4 2.5605 0.7140
NAP1L2 Layer 4 2.5898 0.7132
SH3GL2 Layer 4 2.3555 0.7131
EVL Layer 4 2.3281 0.7115
FAM49A Layer 4 2.5332 0.7113
ZSCAN18 Layer 4 2.4297 0.7112
MEF2C Layer 4 2.2871 0.7105
SCAMP5 Layer 4 2.2773 0.7097
PRDX3 Layer 4 2.4844 0.7095
TRIM37 Layer 4 2.6074 0.7092
GABARAPL1 Layer 5 2.2129 0.7089
NISCH Layer 4 2.3125 0.7088
GUCY1B1 Layer 4 2.5723 0.7084
GLS Layer 4 2.4941 0.7082
TOLLIP Layer 4 2.3555 0.7081
NDUFS1 Layer 4 2.4785 0.7077
EPHA4 Layer 4 3.1113 0.7072
SPIN1 Layer 5 2.3438 0.7071
ATP6V1B2 Layer 4 2.3027 0.7071
HERC1 Layer 4 2.5781 0.7068
CD200 Layer 4 2.5723 0.7068
PJA2 Layer 4 2.1543 0.7066
UBE2E3 Layer 4 2.7480 0.7065
HSPA12A Layer 3 2.3281 0.7064
TUBB3 Layer 3 2.3926 0.7063
NDUFV2 Layer 4 2.2969 0.7062
MAPK10 Layer 4 2.3809 0.7061
CEND1 Layer 4 2.5176 0.7058
TMEM30A Layer 4 2.1973 0.7053
MAP1LC3B Layer 3 2.3242 0.7051
NMNAT2 Layer 4 2.3652 0.7048
SLC25A4 Layer 4 2.3867 0.7045

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1974
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1974_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1974/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1974/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1974/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1974/report/PD/BN1974_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1974/report/PD/BN1974_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 10:26:37
  • Number of Processes: 10
  • Spending Time: 0h 5m